Contacts of the strand formed by residues 363 - 371 (chain B) in PDB entry 5YL4
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with MET 363 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272B PRO* 3.8 10.7 - - - +
283B ALA* 4.5 12.4 - - + +
284B LEU* 3.5 33.0 + - - +
285B THR* 4.8 0.2 - - - -
286B VAL* 3.8 31.6 - - + +
289B LEU* 3.7 27.1 - - + +
318B ARG 3.2 15.5 - - - +
319B GLY* 4.3 2.0 - - - -
320B ARG 4.2 9.9 - - - +
321B MET* 3.8 23.1 - - + -
357B PRO* 5.1 1.1 - - - -
358B PRO* 5.6 0.2 - - - -
361B LEU* 3.3 6.2 - - - +
362B LYS* 1.3 85.4 - - + +
364B SER* 1.3 62.1 + - - +
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Residues in contact with SER 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B PHE* 3.7 21.4 - - - -
271B ALA 3.2 13.7 - - - -
272B PRO* 4.2 4.0 - - - -
289B LEU* 3.8 8.9 - - - +
317B PHE* 3.5 1.9 - - - -
318B ARG* 2.8 40.4 + - - +
358B PRO* 3.4 29.7 - - - +
361B LEU* 4.3 4.0 - - - -
363B MET* 1.3 74.7 - - - +
365B ALA* 1.3 64.7 + - - +
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Residues in contact with ALA 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B PHE* 3.4 5.8 - - - -
271B ALA* 2.8 38.2 + - + +
289B LEU* 4.1 12.8 - - + +
293B MET* 3.4 31.5 - - + +
316B ILE 3.6 5.8 - - - -
317B PHE* 3.8 19.7 - - + -
364B SER* 1.3 78.5 - - - +
366B THR* 1.3 62.3 + - - +
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Residues in contact with THR 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B THR* 4.1 13.0 - - + +
235B GLY* 3.0 42.3 - - - -
236B VAL* 4.0 18.4 - - + +
269B GLY 3.5 11.2 - - - +
270B PHE* 3.3 17.0 - - - -
293B MET* 3.2 6.9 - - - +
315B ALA* 3.4 2.8 - - - -
316B ILE* 3.0 39.7 + - + +
318B ARG* 5.6 2.6 - - - +
365B ALA* 1.3 69.9 - - - +
367B PHE* 1.3 64.6 + - - +
368B ILE* 4.2 2.3 + - + +
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Residues in contact with PHE 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B MET* 3.6 13.0 - - + -
268B PRO* 3.4 6.4 - - - +
269B GLY* 2.8 46.6 + - - +
293B MET* 3.6 43.5 - - + +
294B PHE* 3.7 21.1 - + - -
299B MET* 3.9 20.4 - - + -
310B TYR* 3.4 33.4 - + - -
313B VAL* 3.4 25.1 - - + -
314B ALA 3.9 2.5 - - - -
315B ALA* 5.2 0.7 - - + -
366B THR* 1.3 74.0 - - - +
368B ILE* 1.3 62.5 + - - +
369B GLY* 3.6 21.5 - - - -
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Residues in contact with ILE 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B TYR* 3.7 13.0 - - + +
236B VAL* 3.6 27.6 - - + -
257B MET* 3.7 14.5 - - + +
266B PHE* 3.6 33.2 - - + -
267B MET 4.2 1.6 - - - -
268B PRO* 4.9 1.6 - - + -
313B VAL* 3.5 4.2 - - - +
314B ALA* 2.9 42.4 + - + +
316B ILE* 4.9 4.9 - - + -
366B THR* 4.8 4.0 - - + +
367B PHE* 1.3 78.9 - - - +
369B GLY* 1.3 58.8 + - - +
506B 8WR 3.4 46.0 - - + +
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Residues in contact with GLY 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B PHE* 3.3 5.0 - - - -
267B MET* 2.7 46.7 + - - +
310B TYR* 4.2 6.5 - - - -
312B THR 4.1 3.8 - - - -
313B VAL* 4.8 0.4 - - - -
367B PHE* 3.6 22.8 - - - -
368B ILE* 1.3 73.5 - - - +
370B ASN* 1.3 60.9 + - - -
371B SER 3.5 3.3 + - - -
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Residues in contact with ASN 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B MET* 3.0 23.2 + - + +
258B VAL* 4.4 0.4 - - - +
259B PRO* 4.0 8.7 - - - +
263B LEU 3.3 25.5 + - - +
265B PHE 4.4 6.2 - - - +
266B PHE* 3.5 27.0 - - + -
310B TYR* 3.8 1.1 - - - -
311B LEU* 2.8 43.1 + - - +
312B THR* 3.1 27.3 + - - +
368B ILE 4.1 1.2 + - - -
369B GLY* 1.3 69.8 - - - -
371B SER* 1.3 61.1 + - - +
422B TYR* 4.8 3.6 - - - -
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Residues in contact with SER 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B PHE 4.8 1.6 + - - +
267B MET* 3.9 19.9 - - - +
305B PRO* 4.6 4.6 + - - +
308B GLY 4.4 1.0 - - - -
309B ARG 3.6 14.8 + - - -
310B TYR* 3.8 25.5 - - - -
311B LEU* 5.2 0.4 - - - -
369B GLY 3.5 3.8 + - - -
370B ASN* 1.3 78.6 - - - +
372B THR* 1.3 64.7 + - - +
373B ALA* 3.0 21.2 + - - +
374B ILE* 3.3 23.9 + - - +
422B TYR* 4.2 3.0 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il